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{{Coexpression_clusters
{
|full_id=C351_Fibroblast_Smooth_mesenchymal_Adipocyte_tenocyte_Synoviocyte_Hair
 

Latest revision as of 11:21, 17 September 2013


Full id: C351_Fibroblast_Smooth_mesenchymal_Adipocyte_tenocyte_Synoviocyte_Hair



Phase1 CAGE Peaks

Hg19::chr14:75070388..75070409,-p@chr14:75070388..75070409
-
Hg19::chr16:4431001..4431014,+p4@VASN
Hg19::chr16:55513074..55513088,+p2@MMP2
Hg19::chr16:55513101..55513124,+p1@MMP2
Hg19::chr16:55516814..55516833,+p@chr16:55516814..55516833
+
Hg19::chr16:55516984..55517009,+p@chr16:55516984..55517009
+
Hg19::chr16:55519282..55519295,+p@chr16:55519282..55519295
+
Hg19::chr16:55519314..55519342,-p@chr16:55519314..55519342
-
Hg19::chr16:55519541..55519560,+p@chr16:55519541..55519560
+
Hg19::chr16:55519569..55519597,+p@chr16:55519569..55519597
+
Hg19::chr16:55519605..55519627,+p@chr16:55519605..55519627
+
Hg19::chr16:55522512..55522527,+p6@MMP2
Hg19::chr16:55522536..55522599,+p4@MMP2
Hg19::chr16:55523690..55523729,-p@chr16:55523690..55523729
-
Hg19::chr16:55525707..55525728,+p@chr16:55525707..55525728
+
Hg19::chr16:55525755..55525774,+p@chr16:55525755..55525774
+
Hg19::chr16:55525781..55525812,+p@chr16:55525781..55525812
+
Hg19::chr16:55527062..55527078,+p7@MMP2
Hg19::chr16:55527084..55527124,+p5@MMP2
Hg19::chr16:55532232..55532249,+p@chr16:55532232..55532249
+
Hg19::chr16:55536741..55536782,+p@chr16:55536741..55536782
+
Hg19::chr16:55539240..55539261,+p@chr16:55539240..55539261
+
Hg19::chr16:55539265..55539280,+p@chr16:55539265..55539280
+
Hg19::chr16:55539338..55539366,+p@chr16:55539338..55539366
+
Hg19::chr16:55539371..55539383,+p@chr16:55539371..55539383
+
Hg19::chr16:55539430..55539443,+p@chr16:55539430..55539443
+
Hg19::chr16:55539539..55539552,+p@chr16:55539539..55539552
+
Hg19::chr16:55539559..55539581,+p@chr16:55539559..55539581
+
Hg19::chr16:55539785..55539877,+p@chr16:55539785..55539877
+
Hg19::chr16:55539883..55539894,+p@chr16:55539883..55539894
+
Hg19::chr16:55539899..55539914,+p@chr16:55539899..55539914
+
Hg19::chr16:55540311..55540323,+p@chr16:55540311..55540323
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0001955blood vessel maturation0.00182503237960673
GO:0004228gelatinase A activity0.00182503237960673
GO:0030574collagen catabolic process0.00762948231814427
GO:0044256protein digestion0.00762948231814427
GO:0044254multicellular organismal protein catabolic process0.00762948231814427
GO:0044266multicellular organismal macromolecule catabolic process0.00762948231814427
GO:0044259multicellular organismal macromolecule metabolic process0.00762948231814427
GO:0044268multicellular organismal protein metabolic process0.00762948231814427
GO:0032963collagen metabolic process0.00762948231814427
GO:0044243multicellular organismal catabolic process0.00762948231814427
GO:0044236multicellular organismal metabolic process0.00762948231814427
GO:0030017sarcomere0.0138075264980836
GO:0021700developmental maturation0.0138075264980836
GO:0030016myofibril0.0138075264980836
GO:0044449contractile fiber part0.014586720778938
GO:0043292contractile fiber0.014586720778938
GO:0007586digestion0.0203692002083057
GO:0001568blood vessel development0.031812593175251
GO:0001944vasculature development0.031812593175251
GO:0004222metalloendopeptidase activity0.0360308646701287



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
muscle tissue5.19e-2164
musculature5.19e-2164
musculature of body5.19e-2164
skeletal muscle tissue8.88e-2162
striated muscle tissue8.88e-2162
myotome8.88e-2162
dense mesenchyme tissue2.56e-2073
somite2.89e-2071
presomitic mesoderm2.89e-2071
presumptive segmental plate2.89e-2071
dermomyotome2.89e-2071
trunk paraxial mesoderm2.89e-2071
paraxial mesoderm1.19e-1972
presumptive paraxial mesoderm1.19e-1972
multilaminar epithelium1.80e-1983
splanchnic layer of lateral plate mesoderm1.89e-1883
epithelial vesicle6.20e-1878
artery9.81e-1842
arterial blood vessel9.81e-1842
arterial system9.81e-1842
trunk mesenchyme8.28e-16122
epithelial tube open at both ends1.57e-1559
blood vessel1.57e-1559
blood vasculature1.57e-1559
vascular cord1.57e-1559
systemic artery8.32e-1533
systemic arterial system8.32e-1533
mesoderm2.90e-14315
mesoderm-derived structure2.90e-14315
presumptive mesoderm2.90e-14315
unilaminar epithelium1.53e-13148
vasculature1.55e-1378
vascular system1.55e-1378
vessel7.68e-1368
mesenchyme9.93e-13160
entire embryonic mesenchyme9.93e-13160
cardiovascular system1.28e-11109
epithelial tube2.01e-11117
circulatory system3.34e-11112
trunk7.63e-10199
aorta1.36e-0921
aortic system1.36e-0921
smooth muscle tissue9.70e-0915
integument4.48e-0846
integumental system4.48e-0846
organism subdivision1.22e-07264
blood vessel smooth muscle1.97e-0710
arterial system smooth muscle1.97e-0710
artery smooth muscle tissue1.97e-0710
aorta smooth muscle tissue1.97e-0710
surface structure4.87e-0799
heart8.34e-0724
primitive heart tube8.34e-0724
primary heart field8.34e-0724
anterior lateral plate mesoderm8.34e-0724
heart tube8.34e-0724
heart primordium8.34e-0724
cardiac mesoderm8.34e-0724
cardiogenic plate8.34e-0724
heart rudiment8.34e-0724
multi-cellular organism8.62e-07656
Disease
Ontology termp-valuen
ovarian cancer2.43e-0814


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.00410848
MA0004.10.085298
MA0006.10.0278021
MA0007.11.42296
MA0009.11.81051
MA0014.10.0792289
MA0017.11.88293
MA0019.10.165418
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.10.130296
MA0029.10.327543
MA0030.10.853787
MA0031.10.270046
MA0038.10.138548
MA0040.10.332103
MA0041.10.312746
MA0042.10.0792314
MA0043.10.39615
MA0046.10.386991
MA0048.10.0192986
MA0050.10.0796249
MA0051.10.136135
MA0052.10.335128
MA0055.10.0162627
MA0056.10
MA0057.10.644104
MA0058.10.0469637
MA0059.10.176465
MA0060.10.0369498
MA0061.10.17251
MA0063.10
MA0066.10.847614
MA0067.10.673046
MA0068.10.0455946
MA0069.10.383853
MA0070.10.374777
MA0071.10.752373
MA0072.12.59632
MA0073.12.12364e-06
MA0074.10.135707
MA0076.10.0525452
MA0077.11.70358
MA0078.10.197204
MA0081.11.53443
MA0083.10.40206
MA0084.10.847335
MA0087.11.71829
MA0088.10.448441
MA0089.10
MA0090.10.461949
MA0091.10.609422
MA0092.10.898018
MA0093.10.0285794
MA0095.10
MA0098.10
MA0100.10.146599
MA0101.10.029437
MA0103.10.491715
MA0105.10.388798
MA0106.10.490178
MA0107.10.570232
MA0108.20.267801
MA0109.10
MA0111.11.27881
MA0113.10.515174
MA0114.10.327715
MA0115.10.603788
MA0116.11.22182
MA0117.10.427006
MA0119.11.93475
MA0122.11.1395
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.142619
MA0139.13.31635
MA0140.10.115685
MA0141.13.84353
MA0142.10.247045
MA0143.10.173319
MA0144.10.293962
MA0145.11.42606
MA0146.10.0015201
MA0147.10.0149049
MA0148.10.660483
MA0149.10.110599
MA0062.20.0234822
MA0035.20.11531
MA0039.20.0128887
MA0138.20.575161
MA0002.20.0936468
MA0137.20.0338658
MA0104.20.0365913
MA0047.20.919009
MA0112.20.0756164
MA0065.20.547406
MA0150.10.0556869
MA0151.10
MA0152.10.379376
MA0153.10.478697
MA0154.10.737639
MA0155.10.440591
MA0156.10.323801
MA0157.10.227782
MA0158.10
MA0159.13.10997
MA0160.11.68729
MA0161.10
MA0162.10.00415725
MA0163.10.00800699
MA0164.10.181076
MA0080.20.11873
MA0018.20.163878
MA0099.20.762621
MA0079.23.41646e-06
MA0102.20.88257
MA0258.10.468988
MA0259.10.0164145
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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